Allan's I/O check and field sensor test is a good place to start. I would also add a list of all alarms with the required indication type and system response (stop equipment, display at local panel, sound alarm horn, etc.). I would include each control loop, and the expected reaction to rising and falling control variables or make/break of each external contact. I would list each setpoint or operator data entry specified, and any trending or data logging. If you have a P & ID (Process and Instrumentation Diagram) I would cross reference each item to a tag number there. Also include verification of each communication link, and each data point to be transmitted to SCADA or PC based HMI.
Each of these should show up on a list, and have a place for sign off by the technicial and the inspector for each item verifying it was tested and the results observed.
In my experience witnessed and fully documented shop testing of anything beyond I/O is a waste of time and money on all but the simplest control systems. Success in a shop does not guarantee success in the field, they are time consuming (i.e. expensive to conduct), difficult to coordinate, and if the fabricator is a crook they can be rigged easily. We do all of the above testing (well, if the contractor isn't screaming for delivery, anyway) in our shop before we ship, but we still jump through a lot of hoops in the field. You inevitably have to play "let's make believe" for some of the sensors and the system responses.
The food and phamrmaceutical industries have some standardized testing protocols that you may be able to get and adapt for your needs.